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Detailed information for vg0323164411:

Variant ID: vg0323164411 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23164411
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.23, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

AGACCTAGCATTGACTGATCAAATTTTAGTACCAGTGTTCACATTTAAACAACGACGGTTCTGTCCACCATCCATTGTGATCCCAAGGATAGCTTCCCGC[T/C]
ATTGAGTCGTCATGGTTTTCTGAGGACGTCCACCTTCCCGCCTCTCAGGAAGTGGCTCCAACAGCATAAAAAACATCATGCAATATCCCATCCCACACAA

Reverse complement sequence

TTGTGTGGGATGGGATATTGCATGATGTTTTTTATGCTGTTGGAGCCACTTCCTGAGAGGCGGGAAGGTGGACGTCCTCAGAAAACCATGACGACTCAAT[A/G]
GCGGGAAGCTATCCTTGGGATCACAATGGATGGTGGACAGAACCGTCGTTGTTTAAATGTGAACACTGGTACTAAAATTTGATCAGTCAATGCTAGGTCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.40%	2.60%	41.58%	11.38%	NA
All Indica	2759	9.30%	4.20%	67.34%	19.14%	NA
All Japonica	1512	99.30%	0.00%	0.60%	0.13%	NA
Aus	269	71.40%	1.50%	26.02%	1.12%	NA
Indica I	595	8.70%	2.20%	74.96%	14.12%	NA
Indica II	465	7.50%	4.50%	68.60%	19.35%	NA
Indica III	913	7.20%	4.70%	62.10%	25.96%	NA
Indica Intermediate	786	13.20%	5.00%	66.92%	14.89%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	98.60%	0.00%	0.99%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	62.20%	3.30%	28.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0323164411	T -> C	LOC_Os03g41690.1	upstream_gene_variant ; 1047.0bp to feature; MODIFIER	silent_mutation	Average:13.955; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0323164411	T -> C	LOC_Os03g41700.1	downstream_gene_variant ; 2713.0bp to feature; MODIFIER	silent_mutation	Average:13.955; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0323164411	T -> C	LOC_Os03g41675-LOC_Os03g41690	intergenic_region ; MODIFIER	silent_mutation	Average:13.955; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0323164411	T -> DEL	N	N	silent_mutation	Average:13.955; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323164411	NA	2.12E-09	mr1663	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323164411	1.94E-06	3.22E-06	mr1847	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251